group arguments (cf0d4aa0) · Commits · github_fork / Chromap

src/chromap.cc

+17 −14

Original line number	Diff line number	Diff line
		@@ -1482,12 +1482,12 @@ uint8_t Chromap<MappingRecord>::GetMAPQ(int num_positive_candidates, int num_neg

		int main(int argc, char *argv[]) {
		cxxopts::Options options("chromap", "A short read mapper for chromatin biology");
		options
		.add_options()
		("i,index-mode", "Build index")
		("m,map", "Map reads")
		options.add_options("Indexing")
		("i,build-index", "Build index")
		("k,kmer", "Kmer length [17]", cxxopts::value<int>())
		("w,window", "Window size [5]", cxxopts::value<int>())
		("w,window", "Window size [5]", cxxopts::value<int>());
		options.add_options("Mapping")
		("m,map", "Map reads")
		("e,error-threshold", "Max # errors allowed to map a read [3]", cxxopts::value<int>())
		("A,match-score", "Match score [1]", cxxopts::value<int>())
		("B,mismatch-penalty", "Mismatch penalty [4]", cxxopts::value<int>())
		@@ -1506,18 +1506,21 @@ int main(int argc, char *argv[]) {
		("allocate-multi-mappings", "Allocate multi-mappings")
		("unique-mappings", "Only output unique mappings")
		("Tn5-shift", "Perform Tn5 shift")
		("BED", "Output mappings in BED/BEDPE format")
		("TagAlign", "Output mappings in TagAlign/PairedTagAlign format")
		("PAF", "Output mappings in PAF format")
		("t,num-threads", "# threads for mapping [1]", cxxopts::value<int>())
		("t,num-threads", "# threads for mapping [1]", cxxopts::value<int>());
		options.add_options("Input")
		("r,ref", "Reference file", cxxopts::value<std::string>())
		("x,index", "Index file", cxxopts::value<std::string>())
		("1,read1", "Single-end read file or paired-end read file 1", cxxopts::value<std::string>())
		("2,read2", "Paired-end read file 2", cxxopts::value<std::string>())
		("b,barcode", "Cell barcode file", cxxopts::value<std::string>())
		("b,barcode", "Cell barcode file", cxxopts::value<std::string>());
		options.add_options("Output")
		("o,output", "Output file", cxxopts::value<std::string>())
		("h,help", "Print help")
		;
		("BED", "Output mappings in BED/BEDPE format")
		("TagAlign", "Output mappings in TagAlign/PairedTagAlign format")
		("PAF", "Output mappings in PAF format");
		options.add_options()
		("h,help", "Print help");

		auto result = options.parse(argc, argv);
		// Optional parameters
		int kmer_size = 17;
		@@ -1755,9 +1758,9 @@ int main(int argc, char *argv[]) {
		}
		}
		} else if (result.count("h")) {
		std::cerr << options.help();
		std::cerr << options.help({"", "Indexing", "Mapping", "Input", "Output"});
		} else {
		std::cerr << options.help();
		std::cerr << options.help({"", "Indexing", "Mapping", "Input", "Output"});
		}
		return 0;
		}

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